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An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping
Abstract Background: There are two main technologies for transcriptome profiling, namely, tiling microarrays and high-throughput sequencing. Recently there has been a tremendous amount of excitement about the latter because of the advent of next-generation sequencing technologies and its promises. Consequently, … Continue reading
ENCODE/modENCODE Consortium Meeting 2009
Ashish Agarwal, LaDeana W. Hillier, Joel Rozowsky, David Koppstein, Andrea Sboner, Lukas Habegger, Jeanyoung Jo, Michael Snyder, Philip Green, Valerie Reinke, Robert H. Waterston, Mark Gerstein, “Transcriptome comparison between tiling arrays and next generation sequencing on matched worm samples, towards … Continue reading
Linear coupled component automata for MILP modeling of hybrid systems
Abstract We ï¬rst introduce a novel modeling framework, called linear coupled component automata (LCCA), to facilitate the modeling of discrete-continuous dynamical systems with piecewise constant derivatives. Second, we provide a procedure for transforming models in this framework to mixed-integer linear … Continue reading
tYNA: An Online Tool for Analysis of Biological Networks
A summary of Kevin Yip’s tYNA software is available here.
Dissertation: Logical Modeling Frameworks for the Optimization of Discrete-Continuous Systems
Abstract Often, it is very difficult to pose a model for a system even after the system is conceptually understood. The reason is the mathematical languages we employ have few forms of expression. We define more expressive languages, first for … Continue reading
Posted in Presentations, Publications
Tagged Hybrid Systems, Optimization, SML, Types
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Finished my PhD!
Thanks to my great advisors Robert Harper and Ignacio Grossmann. Read all about it here.
Milner on the science of the artificial
“Probably what [physicists] mean is: [computer science] can’t be a science because we are always making things. What are we doing science of? We are doing the science of our own constructions. But I think the boundary between understanding one’s … Continue reading
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Boltzmann says theory is practical
“Nothing is more practical than a good theory.” — Ludwig Boltzmann
